The journey of young Charles Darwin aboard His Majesty's Ship Beagle, during the years 1831-36, is one of the best known and most neatly mythologized episodes in the history of science. As the legend goes, Darwin sailed as ship's naturalist on the Beagle, visited the Galápagos archipelago in the eastern Pacific Ocean, and there beheld giant tortoises and finches. The finches, many species of them, were distinguishable by differently shaped beaks, suggesting adaptations to particular diets. The tortoises, island by island, carried differently shaped shells.

These clues from the Galápagos led Darwin (immediately? long afterward? here the mythic story is vague) to conclude that Earth's living diversity has arisen by an organic process of descent with modification—evolution, as it's now known—and that natural selection is the mechanism. He wrote a book called The Origin of Species and persuaded everyone, except the Anglican Church establishment, that it was so.

Well, yes and no. This cartoonish account of the Beagle voyage and its consequences contains a fair bit of truth, but it also confuses, distorts, and omits much. For instance, the finches weren't as illuminating as the diversity of the islands' mockingbirds, at least not initially, and Darwin couldn't make sense of them until a bird expert back in England helped. The Galápagos stopover was a brief anomaly near the end of an expedition devoted mostly to surveying the South American coastline. Darwin hadn't signed on to the Beagle as its official naturalist; he was a 22-year-old Cambridge graduate pointed rather indifferently toward a career as a country clergyman, invited on the voyage as a dining companion for the captain, a mercurial young aristocrat named Robert Fitzroy. Darwin did assume the role of naturalist, and think of himself that way, as time went on. But his theory developed slowly, secretively, and The Origin of Species (full title: On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life) didn't appear until 1859. Many scientists, along with some Victorian clergymen, resisted its evidence and arguments for decades afterward. The reality of evolution became widely accepted during Darwin's lifetime, but his particular theory—with natural selection as prime cause—didn't triumph until about 1940, after it had been successfully integrated with genetics.

Apart from those clarifications, the most interesting point missed by the simplified tale is this: Darwin's first real clue toward evolution came not in the Galápagos but three years before, on a blustery beach along the north coast of Argentina. And it didn't take the form of a bird's beak. It wasn't even a living creature. It was a trove of fossils. Never mind the notion of Darwin's finches. For a fresh view of the Beagle voyage, start with Darwin's armadillos and giant sloths.

In September 1832, during the first year of its mission, the Beagle anchored near Bahía Blanca, a settlement at the head of a bay about 400 miles southwest of Buenos Aires. A certain General Rosas was waging a genocidal war against the Indians, and Bahía Blanca stood as a fortified outpost, occupied mostly by soldiers. For more than a month the Beagle remained in that area, some of its crew occupied with surveying, others assigned to shore duties—digging a well, gathering firewood, hunting for meat. The landscape round about was classic Argentine Pampas, fertile grassland, giving way to grass-anchored sand dunes along the coast. The hunters brought back deer, agoutis, and other game, including several armadillos and a large flightless bird Darwin loosely called an "ostrich." Of course it wasn't an ostrich (which is native to Africa, and formerly the Middle East); it was a rhea, specifically Rhea americana, ostrichlike in appearance but endemic to South America and the heaviest bird on the continent.

"What we had for dinner to day would sound very odd in England," Darwin wrote in his diary on September 18, reveling in the exoticism of his new regimen: "Ostrich dumpling & Armadilloes." He was out for a romping adventure, not just a natural history field trip, and his shipboard diary (later transformed into a travel book that came to be known as The Voyage of the Beagle) reflects his attention to cultures, peoples, politics, as well as to science. The red meat of the big bird resembled beef, he recorded. The armadillos, peeled out of their shells, tasted and looked like ducks. His culinary experiences here on the Pampas, and later in Patagonia, besides being part of his voracious tour of discovery, would eventually play a role in his evolutionary thinking.

A few days afterward, on September 22, 1832, Darwin and Fitzroy took a small boat to visit a site called Punta Alta, ten miles from their anchor­age, where they found some rocky outcrops overlooking the water. "These are the first I have seen," Darwin wrote, "& are very interesting from containing numerous shells & the bones of large animals."

Despite the name, Punta Alta ("high point") was not very high, its reddish mudstone cliff rising only about 20 feet. But if the headland wasn't dramatic, the exposed fossils were: big shapes, unusual shapes, and abundant. Darwin and a helper went to work on the soft rock with pickaxes. Between that session and later efforts, he harvested from Punta Alta the remains of nine great mammals, all unknown or barely known to science. They were extinct Pleistocene giants, unique to the Americas in an age sometime before 12,000 years ago.

The most famous of them was Megatherium, an elephant-size ground sloth that had already been named and described by the French anatomist Georges Cuvier on the basis of one set of fossils found in Paraguay. Living sloths are native to Central and South America, and only there; Megatherium shared many of their anatomical traits but was far too large for climbing trees. Darwin's finds also included at least three other giant ground sloths, an extinct form of horse, and a protective carapace of small bony scutes fitted closely together, remnant from some big beast that must have strongly resembled an armadillo. He was already familiar with flesh-and-blood armadillos, having eaten those shucked, ducky ones with his ostrich dumplings. He had also watched local gauchos kill armadillos and roast them in the shells. Of the 20 species of living armadillo, all are confined to the Americas and several are common on the Pampas; the roasted animals may have been six-banded armadillos (Euphractus sexcinctus), plentiful thereabouts and reputed to taste terrible, which might not have dissuaded those unfussy gauchos, who sometimes lived off the land for weeks. "Like to snails, all their property is on their backs & their food around them," Darwin wrote, referring to the cowboys, not the armadillos.

A month later, 30 miles up the coast from Punta Alta, Darwin discovered another fossil-rich sea cliff, this one rising 120 feet and marking a place called Monte Hermoso. There he unearthed the stony remains of several gnawing creatures, which variously put him in mind of an agouti, a capybara, and a smaller South American rodent, the tuco-tuco, except that again, in each case, the match between fossil and living species was close but not identical. Still later and farther south on the Argentine coast, he excavated a third set of mammal bones, which, to an anatomist who eventually examined them, suggested an extinct form of camel. That creature became known as Macrauchenia. The camel family includes two wild South American species, the guanaco and the vicua, as well as their domesticated forms, the llama and the alpaca. Darwin was well aware that living guanacos inhabited that area, having shot one himself just days earlier.

These discoveries, analogies, and juxtapositions went into his memory and imagination, to ferment there as the voyage continued and for years afterward. Meanwhile the fossils themselves were crated up for shipping back to England, mostly to the care of John Stevens Henslow, the gentle botanist who had been Darwin's mentor at Cambridge.

"I have been lucky with fossil bones," he told Henslow in a letter. He mentioned the giant rodent, the ground sloths, and the section of bony polygonal scutes, commenting on the last: "Immediately I saw them I thought they must belong to an enormous Armadillo, living species of which genus are so abundant here." And he added: "If it interests you sufficiently to unpack them, I shall be very curious to hear something about them."

It's important not to overstate how clearly Darwin could even identify, let alone interpret, what he had found. Most of his fossils, apart from the Megatherium, represented species not yet familiar to experts, and he was no expert. He wasn't a comparative anatomist, like the great Cuvier; he wasn't especially knowledgeable about mammals; and the very word "paleontologist" hadn't yet come into use. Darwin entrusted the description and identification of his fossils to a brilliant young anatomist back in London named Richard Owen, an up-and-coming authority on extinct mammals. It was Owen who gave names to the unknown sloths, and Owen who suggested (mistakenly, later correcting himself) the affinity between Macrauchenia and a camel.

Darwin himself was no Owen. He was just a highly attentive fieldman, greedy for specimens, learning as he went. The Beagle invitation had rescued him from an unsuitable future as a country pastor, and since his first days aboard ship he had applied himself diligently, maturing fast to assume (and then transcend) the role of ship's naturalist. His best qualifications for interpreting the fossils were his intense curiosity, his talent for close observation, and his instinctive sense that everything in the natural world is somehow connected with everything else. Also, he wasn't afraid to speculate boldly—so long as he could do it in private.

Another small but suggestive datum reached him months later, while the Beagle lingered off northern Patagonia and Darwin spent time ashore among another congenial group of gauchos. First it was hearsay: The gauchos mentioned a rare form of ostrich, smaller than the common one, with shorter legs, and more easily killed using their bolas, but otherwise similar. The possibility of finding that bird slipped Darwin's mind until one of his shipmates shot such a smaller "ostrich" (another rhea) for its meat. Darwin paid little attention, assuming it was a juvenile. "The bird was skinned and cooked before my memory returned," he wrote, in a passage so candid you can almost see him smacking his forehead with a palm. "But the head, neck, legs, wings, many of the larger feathers, and a large part of the skin, had been preserved." He rescued those scraps and sent them to England, where they were stitched into a presentable specimen for the museum of the Zoological Society. The ornithologist John Gould, to whom Darwin would consign his Galápagos finches and mockingbirds for identification, also got a first look at this creature. Gould confirmed that it was a distinct species and called it Rhea darwinii (a name later changed because of taxonomic technicalities) for the man who had rescued it from the midden.

What intrigued Darwin most about the two rhea species was that, similar as they were, they overlapped very little in geographic distribution. The greater rhea inhabited the Pampas and northern Patagonia, as far south as Argentina's Río Negro, which drained to the coast at about 41° south latitude; the lesser rhea replaced it beyond the Río Negro and occupied southern Patagonia. Together with the evidence of extinct South American mammals, the implications of rhea diversity and distribution would prove almost as suggestive to Darwin as the patterns he would later find among the finches and mockingbirds of the Galápagos.

How do species originate, and how do they come to be where they are? The orthodox story, still firmly embraced by European science at the time of the Beagle voyage, was that God had created species independently, in sequential batches (to compensate for extinctions), and had chosen to place them, almost arbitrarily, in their particular locales—kangaroos in Australia, giraffes and zebras in Africa, rheas and sloths and armadillos in South America, extinct and living forms clustered closely in space and time. But to Darwin, both the extinct mammals (along with their living counterparts among sloths and armadillos) and the two rheas (occupying adjacent regions of habitat) suggested something more rational: the ideas of relatedness and succession among closely allied species. The living tree sloths and armadillos seemed to have succeeded earlier such forms in time, inhabiting roughly the same terrain during different epochs of Earth's history. (Those earlier forms of sloth were true sloths; the earlier armored creatures are now known as glyptodonts, a family distinct from but closely related to living armadillos.) The two rheas, similar but not identical, likewise seemed to succeed each other—but in space, across the horizontal dimension of landscape. The clustering in time and in space thus hinted that each group had descended, with modification, from common ancestors: rheas from rheas, sloths from earlier sloths, armadillos from an armadilloish or glyptodontish precursor, possibly far larger than armadillos living today. That's the explanation to which Darwin felt drawn, because it seemed more economical, more inductive, and more persuasive than the creationist scenario.

How important were the South American data in shaking his faith in the orthodox view—persuading him that evolution was a reality for which he should seek a material explanation? Darwin himself would give several answers to that question over the length of his lifetime. His answers ranged, in essence, from very important, but less so than the Galápagos birds, to crucially important, period.

He hinted at the subject in 1845, in the second edition of his Beagle narrative, revised by him to include coy hints about the theory he was still unprepared to publish. The relationships between fossil and living forms among the rodents, the sloths, the camels, and the armadillos were "most interesting facts," he noted. Further work by other investigators had meantime revealed the same kind of pattern in Brazil—fossil and living forms of anteater, of tapir, of monkey and peccary and possum. "This wonderful relationship in the same continent between the dead and the living," Darwin wrote, would "throw more light on the appearance of organic beings on our earth, and their disappearance from it, than any other class of facts." But what sort of light? What would that light reveal? Throwing light was one of his favorite meta­phors, and it would return, but not for a dec­ade and a half—not until he was ready to shine the blinding beam of his theory in public.

There's another intriguing question about the South American fossils and rheas: When did this evidence register on Darwin, tipping him toward the idea of evolution? The widely accepted view is that he returned from the Beagle voyage not yet an evolutionist, merely puzzled by what he had seen, and that he made the big leap to evolutionary thinking after his consultations in London, with John Gould and Richard Owen, about the bird and fossil specimens he had consigned to them. (Soon after that he began using a new term for the process: "transmutation.") But not everyone agrees.

"I think he was personally converted much earlier," a historian of paleontology named Paul D. Brinkman told me. We were sitting in his office at the North Carolina Museum of Natural Sciences in Raleigh, amid a portrait of young Darwin, a Jurassic Park poster, and photos of old ground sloth and glyptodont specimens. "Why would there be this resemblance between the fossil fauna and the extant fauna of this area? Why would they be so similar?" he asked, repostulating questions that Darwin must have framed. The ancient rodents and the living agoutis, the glyptodonts and the armadillos—why? "I think one of the possible explanations he was mulling over, even as early as 1832, was that one begat the other. Transmutation." But even Brinkman admits that there is only tenuous evidence, "no smoking gun," for his hypothesis about Darwin having converted to evolutionism long before ever striding ashore in the Galápagos.

One cryptic piece of testimony came from Darwin himself, near the end of his life, in the private autobiography he wrote for his family. "During the voyage of the Beagle," he reminisced, "I had been deeply impressed by discovering in the Pampean formation great fossil animals covered with armour like that on the existing armadillos." He alluded also to the rheas and to the Galápagos species, differing island by island. "It was evident," Darwin wrote, "that such facts as these, as well as many others, could be explained on the supposition that species gradually become modified; and the subject haunted me." In years since, it has also haunted scholars.

The Beagle, having completed its South American survey work and then spent a year circumnavigating the world, reached England in October 1836. Darwin, then 27 and a seasoned naturalist, weary of travel, eager for home, was a changed man in other ways too. He no longer saw himself serving time in a country parsonage; he was committed to a life of science. And he had at least started to lose his belief in the immutability of species. It's not possible to know with certainty, but he seems by then to have identified the great question, though not yet the great answer, that would dominate the rest of his working life.

With his specimens outsourced for expert identification—the birds to Gould, the fossil mammals to Owen, the reptiles to a zoologist named Thomas Bell—he set about putting his thoughts in order and following out his suspicions. He brainstormed in his most private notebook about ostriches, guanacos, and whether "one species does change into another." If so, how might such transmutation occur? About a year and a half later, after adding one crucial piece to his thinking (the idea of excess reproduction and struggle for existence, adopt­ed from an essay on human population by Thomas Malthus), Darwin hit upon his theory: natural selection, whereby the best adapted individuals of each population survive to leave offspring and others don't. Then he nurtured, refined, developed, and concealed that theory for 20 years, until a younger man named Alfred Russel Wallace (see "The Man Who Wasn't Darwin" in National Geographic, December 2008) struck upon the same idea, forcing Darwin to rush to get his own ready for print.

That was 1858. By then Darwin had begun writing a long, detailed, heavily footnoted treatise on natural selection, but it was only half finished. Panicked, feeling proprietary, yet also reawakened to the wondrous immediacy of the story he had to tell, he shoved the big book aside and quickly composed a more streamlined account. This shorter, slapdash version would be merely an "abstract" of the theory and its supporting data, he claimed. He called it "my abominable volume" because, after decades of cogitation and delay, the writing process was so hurried and painful. He wanted to title it An Abstract of an Essay on the Origin of Species and Varieties Through Natural Selection, but his publisher persuaded him to accept something at least marginally more snappy. It appeared in November 1859, titled On the Origin of Species by Means of Natural Selection et cetera, and was a sellout success immediately.

Five more editions went to print during Darwin's lifetime. Almost inarguably, it's the most significant single scientific book ever published. After 150 years, people still venerate it, people still deplore it, and The Origin of Species continues to exert an extraordinary influence—though, unfortunately, not many people actually read it.

And the forgotten clues that led him to his theory are still largely forgotten. Anyway, they're omitted from the mythic account. Scholars still dispute the significance of those extinct and living Argentine creatures, especially the ground sloths and glyptodonts, the tree sloths and armadillos and rheas. Evidence is mixed, even among the various comments on the matter left behind by Darwin himself. The most telling of those comments, in my view, is one so conspicuously placed that it tends to get overlooked. It comprises the first two sentences of The Origin of Species, beginning the book on a nostalgic note. It says:

"When on board H.M.S. 'Beagle,' as naturalist, I was much struck with certain facts in the distribution of the inhabitants of South America, and in the geological relations of the present to the past inhabitants of that continent. These facts seemed to me to throw some light on the origin of species. …"

The finches of the Galápagos make their appearance about 400 pages later.